During her first reign the Soga clan seized power. Her son Naka no Ōe planned a coup d'état and slew Soga no Iruka at the court in front of her throne. The Empress, shocked by this incident, abdicated the throne.

Kōgyoku's contemporary title would not have been tennō, as most historians believe this title was not introduced until the reigns of Emperor Tenmu and Empress Jitō. Rather, it was presumably Sumeramikoto or Amenoshita Shiroshimesu Ōkimi (治天下大王), meaning "the great queen who rules all under heaven". Alternatively, Kōgyoku might have been referred to as (ヤマト大王/大君) or the "Great Queen of Yamato".

Empress Kōgyoku reigned for four years. The years of Kōgyoku's reign are not linked by scholars to any era or nengō.[9] The Taika era innovation of naming time periods – nengō – was yet to be initiated during her son's too-brief reign.

In this context, Brown and Ishida's translation of Gukanshō offers an explanation about the years of Empress Jitō's reign which muddies a sense of easy clarity in the pre-Taiho time-frame:

"The eras that fell in this reign were: (1) the remaining seven years of Shuchō [(686+7=692?)]; and (2) Taika, which was four years long [695–698]. (The first year of this era was kinoto-hitsuji [695].) ... In the third year of the Taka era [697], Empress Jitō yielded the throne to the Crown Prince."[10]

The years of Kōgyoku's reign are not more specifically identified by more than one era name or nengō which was an innovation of Kōtoku's brief reign.[11]

When Kōtoku died, his designated heir was Naka no Ōe. When Naka no Ōe's mother re-ascended, he continued in the role of her heir and crown prince. In this role, he could and did remain active in the political life of Japan.

In the fifth year of Saimei's reign, Paekche in Korea was destroyed in 660. Japan assisted Paekche loyals in an attempt to aid the revival of Paekche dynasty. Early in 661, Saimei responded to the situation by leaving her capital in Yamato Province. Her plan was to lead a military expedition to Korea. The empress stayed in Ishiyu Temporary Palace in Iyo Province, today Dōgo Onsen. In May she arrived at Asakura Palace in the north part of Tsukushi province in Kyūshū, today a part of Fukuoka Prefecture. The allied army of Japan and Paekche was preparing for war against Silla, but the death of the empress thwarted those plans. In 661, Saimei died in the Asakura Palace before the army departed to Korea. In October her body was brought from Kyūshū by sea to Port Naniwa-zu (today Osaka city); and her state funeral was held in early November.

Empress Saimei ruled for seven years. The years of Saimei's reign are not linked by scholars to any era or nengō.[11] The Taika era innovation of naming time periods – nengō – languished until Mommu reasserted an imperial right by proclaiming the commencement of Taihō in 701.

Kugyō (公卿) is a collective term for the very few most powerful men attached to the court of the Emperor of Japan in pre-Meiji eras.

In general, this elite group included only three to four men at a time. These were hereditary courtiers whose experience and background would have brought them to the pinnacle of a life's career. During Kōgyoku's reign, this apex of the Daijō-kan included:

^Brown, pp. 264; prior to Emperor Jomei, the personal names of the emperors (imina) were very long and people did not generally use them; however, the number of characters in each name diminished after Jomei's reign.